Novel Algorithm for Comparing Phylogenetic Trees with Different but Overlapping Taxa

被引:2
|
作者
Koshkarov, Aleksandr [1 ]
Tahiri, Nadia [1 ]
机构
[1] Univ Sherbrooke, Dept Comp Sci, Sherbrooke, PQ J1K 2R1, Canada
来源
SYMMETRY-BASEL | 2024年 / 16卷 / 07期
基金
加拿大自然科学与工程研究理事会;
关键词
phylogenetic tree; evolution; tree distance; tree completion; MAXIMUM AGREEMENT SUBTREE; DISTANCE; METRICS;
D O I
10.3390/sym16070790
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Comparing phylogenetic trees is a prominent problem widely used in applications such as clustering and building the Tree of Life. While there are many well-developed distance measures for phylogenetic trees defined on the same set of taxa, the situation is contrasting for trees defined on different but mutually overlapping sets of taxa. This paper presents a new polynomial-time algorithm for completing phylogenetic trees and computing the distance between trees defined on different but overlapping sets of taxa. This novel approach considers both the branch lengths and the topology of the phylogenetic trees being compared. We demonstrate that the distance measure applied to completed trees is a metric and provide several properties of the new method, including its symmetrical nature in tree completion.
引用
收藏
页数:17
相关论文
共 50 条
  • [1] Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review
    Li, Wanlin
    Koshkarov, Aleksandr
    Tahiri, Nadia
    ECOLOGY AND EVOLUTION, 2024, 14 (08):
  • [2] A randomized algorithm for comparing sets of phylogenetic trees
    Sul, Seung-Jin
    Williams, Tiffani L.
    PROCEEDINGS OF THE 5TH ASIA- PACIFIC BIOINFOMATICS CONFERENCE 2007, 2007, 5 : 121 - +
  • [3] A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
    Nye, TMW
    Liò, P
    Gilks, WR
    BIOINFORMATICS, 2006, 22 (01) : 117 - 119
  • [4] On the ancestral compatibility of two phylogenetic trees with nested taxa
    Llabres, Merce
    Rocha, Jairo
    Rossello, Francesc
    Valiente, Gabriel
    JOURNAL OF MATHEMATICAL BIOLOGY, 2006, 53 (03) : 340 - 364
  • [5] On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa
    Mercè Llabrés
    Jairo Rocha
    Francesc Rosselló
    Gabriel Valiente
    Journal of Mathematical Biology, 2006, 53 : 340 - 364
  • [6] Comparing the likelihood functions of phylogenetic trees
    Bar-Hen, A
    Kishino, H
    ANNALS OF THE INSTITUTE OF STATISTICAL MATHEMATICS, 2000, 52 (01) : 43 - 56
  • [7] Comparing trees in a phylogenetic relationship repository
    Bluis, J
    Nori, R
    Wang, HW
    Zhou, PL
    Gogarten, JP
    Shin, DG
    2ND ANNUAL IEEE INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, PROCEEDINGS, 2001, : 166 - 173
  • [8] Comparing the Likelihood Functions of Phylogenetic Trees
    A. Bar-Hen
    H. Kishino
    Annals of the Institute of Statistical Mathematics, 2000, 52 : 43 - 56
  • [9] ALGORITHM FOR CONSTRUCTION OF PHYLOGENETIC TREES
    TOHA, J
    SOTO, MA
    CHINGA, H
    ZEITSCHRIFT FUR NATURFORSCHUNG C-A JOURNAL OF BIOSCIENCES, 1989, 44 (3-4): : 312 - 316
  • [10] Stochastic models for phylogenetic trees on higher-order taxa
    Aldous, David
    Krikun, Maxim
    Popovic, Lea
    JOURNAL OF MATHEMATICAL BIOLOGY, 2008, 56 (04) : 525 - 557